Éditeur(s) : Springer
Résumé : Batch culture experiments using viral enrichment were conducted to test the response of a coastal bacterial community to autochthonous (i.e., co-existing) or allochthonous riverine viruses. The effects of viral infections on bacterial dynamics and activity were assessed by epifluorescence microscopy and thymidine incorporation, respectively, whereas the effect of viral infection on bacterial community composition was examined by polymerase chain reaction-single strand conformation polymorphism 16S ribosomal RNA fingerprinting. The percentages of high nucleic acid-containing cells, evaluated by flow cytometry, were significantly correlated (r (2) = 0.91, n = 12, p < 0.0001) to bacterial production, making this value a good predictor of active cell dynamics along the study. While confinement and temperature were the two principal experimental factors affecting bacterial community composition and dynamics, respectively, additions of freshwater viruses had significant effects on coastal bacterial communities. Thus, foreign viruses significantly reduced net bacterial population increase as compared to the enrichment treated with inactivated virus. Moreover, freshwater viruses recurrently and specifically affected bacterial community composition, as compared to addition of autochthonous viruses. In most cases, the combined treatment viruses and freshwater dissolved organic matter helped to maintain or even enhance species richness in coastal bacterial communities in agreement to the 'killing the winner' hypothesis. Thus, riverine virus input could potentially influence bacterial community composition of the coastal bay albeit with modest modification of bulk bacterial growth.
Microbial Ecology (0095-3628) (Springer), 2009-02 , Vol. 57 , N. 2 , P. 295-306

Droits : 2009 Springer
http://archimer.ifremer.fr/doc/2009/publication-6636.pdf
DOI:10.1007/s00248-008-9428-1
http://archimer.ifremer.fr/doc/00000/6636/

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
Type IB DNA topoisomerases can eliminate torsional stresses produced during replication and transcription. These enzymes are found in all eukaryotes and a short version is present in some bacteria and viruses. Among prokaryotes, the long eukaryotic version is only observed in archaea of the phylum Thau-marchaeota. However, the activities and the roles of these topoisomerases have remained an open question. Here, we demonstrate that all available thaumar-chaeal genomes contain a topoisomerase IB gene that defines a monophyletic group closely related to the eukaryotic enzymes. We show that the topIB gene is expressed in the model thaumarchaeon Ni-trososphaera viennensis and we purified the recom-binant enzyme from the uncultivated thaumarchaeon Candidatus Caldiarchaeum subterraneum. This enzyme is active in vitro at high temperature, making it the first thermophilic topoisomerase IB characterized so far. We have compared this archaeal type IB enzyme to its human mitochondrial and nuclear counterparts. The archaeal enzyme relaxes both negatively and positively supercoiled DNA like the eukaryotic enzymes. However, its pattern of DNA cleavage specificity is different and it is resistant to camptothecins (CPTs) and non-CPT Top1 inhibitors, LMP744 and lamellarin D. This newly described ther-mostable topoisomerases IB should be a promising new model for evolutionary, mechanistic and structural studies.
ISSN: 0305-1048

Droits : http://creativecommons.org/licenses/by/
hal-01327354
http://hal.upmc.fr/hal-01327354
http://hal.upmc.fr/hal-01327354/document
http://hal.upmc.fr/hal-01327354/file/Nucl.%20Acids%20Res.-2016-Dahmane-2795-805.pdf
DOI : 10.1093/nar/gkw097

Éditeur(s) : Elsevier
Résumé : In biological modelling of the coastal phytoplankton dynamics, the light attenuation coefficient is often expressed as a function of the concentrations of chlorophyll and mineral suspended particulate matter (SPM). In order to estimate the relationship between these parameters over the continental shelf of the northern Bay of Biscay, a set of in situ data has been gathered for the period 1998-2003 when SeaWiFS imagery is available. These data comprise surface measurements of the concentrations of total SPM, chlorophyll, and irradiance profiles from which is derived the attenuation coefficient of the photosynthetically available radiation, K-PAR. The performance of the IFREMER look-up table used to retrieve the chlorophyll concentration from the SeaWiFS radiance is evaluated on this new set of data. The quality of the estimated chlorophyll concentration is assessed from a comparison of the variograms of the in situ and satellite-derived chlorophyll concentrations. Once the chlorophyll concentration is determined, the non living SPM, which is defined as the SPM not related to the dead or alive endogenous phytoplankton, is estimated from the radiance at 555 nm by inverting a semi-analytic model. This method provides realistic estimations of concentrations of chlorophyll and SPM over the continental shelf all over the year. Finally, a relationship, based on non living SPM and chlorophyll, is proposed to estimate K-PAR on the continental shelf of the Bay of Biscay. The same formula is applied to non living SPM and chlorophyll concentrations, observed in situ or derived from SeaWiFS radiance.
Remote Sensing of Environment (0034-4257) (Elsevier), 2005-03 , Vol. 95 , N. 1 , P. 29-46

Droits : 2004 Elsevier Inc. All rights reserved
http://archimer.ifremer.fr/doc/2005/publication-1172.pdf
DOI:10.1016/j.rse.2004.11.007
http://archimer.ifremer.fr/doc/00000/1172/

Résumé : Au cours de cette étude, nous avons étudié l'impact de la biodéposition sur les bassins conchylicoles. La biodéposition constitue un "concentrateur" de particules fines au niveau du sédiment. Cet impact est particulièrement évident sur les sédiments sableux et concerne la granulométrie, les taux de matière organique, la concentration des métaux et des hydrocarbures. Une étude comparée est faite entre estran sableux et bassin de type "claire" à sédiment argileux. L'impact de la biodéposition sur les sédiments sableux n'est pas irréversible. Le bassin fermé avec un sédiment argileux agit comme un concentrateur-rétenteur de particules et des contaminants potentiels. Ceci souligne le rôle "tampon" des marais maritimes entre milieu continental et milieu marin.

Droits : 1989 Ifremer
http://archimer.ifremer.fr/doc/00076/18757/16327.pdf
http://archimer.ifremer.fr/doc/00076/18757/

Éditeur(s) : Elsevier
Résumé : Previous studies conducted on the continental shelf in the Southeast Bay of Biscay influenced by Gironde waters (one of the two largest rivers on the French Atlantic coast) showed the occurrence of late winter phytoplankton blooms and phosphorus limitation of algal growth thereafter. In this context, the importance of dissolved organic phosphorus (DOP) for both algae and bacteria was investigated in 1998 and 1999 in terms of stocks and fluxes. Within the mixed layer, although phosphate decreased until exhaustion from winter to spring, DOP remained high and phosphate monoesters made up between I I to 65% of this pool. Total alkaline phosphatase activity (APA, V-max) rose gradually from winter (2-8 nM h(-1)) to late spring (100-400 nM h-1), which was mainly due to an increase in specific phytoplankton (from 0.02 to 3.0 nmol mu gC(-1) h(-1)) and bacterial APA (from 0.04 to 4.0 nmol mu gC(-1) h(-1)), a strategy to compensate for the lack of phosphate. At each season, both communities had equal competitive abilities to exploit DOP but, taking into account biomass, the phytoplankton community activity always dominated (57-63% of total APA) that of bacterial community (9-11%). The dissolved APA represented a significant contribution. In situ regulation of phytoplanktonic APA by phosphate (induction or inversely repression of enzyme synthesis) was confirmed by simultaneously conducted phosphate-enrichment bioassays. Such changes recorded at a time scale of a few days could partly explain the seasonal response of phytoplankton communities to phosphate depletion.
Journal of Experimental Marine Biology and Ecology (0022-0981) (Elsevier), 2005-05 , Vol. 318 , N. 2 , P. 213-225

Droits : 2005 Elsevier B.V. All rights reserved
http://archimer.ifremer.fr/doc/2005/publication-608.pdf
DOI:10.1016/j.jembe.2004.12.017
http://archimer.ifremer.fr/doc/00000/608/

Éditeur(s) : Elsevier
Résumé : Seasonal variations in nutrient inputs are described for the main rivers (Loire and Vilaine) flowing into the northern Bay of Biscay. The river plumes are high in N/P ratio in late winter and spring, but not in the inner plume during the summer. Conservative behavior results in most nutrients entering the estuary and eventually reaching the coastal zone. Temporal and spatial aspects of phytoplankton growth and nutrient uptake in the northern Bay of Biscay distinguish the central area of salinity 34 from the plume area. The first diatom bloom appears offshore in late winter, at the edge of the river plumes, taking advantage of haline stratification and anticyclonic "weather windows." In spring, when the central area of the northern shelf is phosphorus-limited, small cells predominate in the phytoplankton community and compete with bacteria for both mineral and organic phosphorus. At that period, river plumes are less extensive than in winter, but local nutrient enrichment at the river mouth allows diatom growth. In summer, phytoplankton become nitrogen-limited in the river plumes; the central area of the shelf is occupied by small forms of phytoplankton, which are located on the thermocline and use predominantly regenerated nutrients.
Journal of Marine Systems (0924-7963) (Elsevier), 2008-07 , Vol. 72 , N. 1-4 , P. 309-319

Droits : 2008 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2007/publication-2354.pdf
DOI:10.1016/j.jmarsys.2007.03.010
http://archimer.ifremer.fr/doc/00000/2354/